Starting phenix.real_space_refine
on Sat May 10 07:19:54 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/8yi7_39311/05_2025/8yi7_39311_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yi7_39311/05_2025/8yi7_39311.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.57
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yi7_39311/05_2025/8yi7_39311.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yi7_39311/05_2025/8yi7_39311.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yi7_39311/05_2025/8yi7_39311_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yi7_39311/05_2025/8yi7_39311_neut.cif"
  }
  resolution = 3.57
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.049
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      43      5.16       5
     C    3514      2.51       5
     N     943      2.21       5
     O    1086      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 49 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 5586
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1485
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 185, 1485
          Classifications: {'peptide': 185}
          Link IDs: {'PTRANS': 6, 'TRANS': 178}
    Chain: "B"
      Number of atoms: 2413
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 303, 2413
          Classifications: {'peptide': 303}
          Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 288}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 764
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 764
          Classifications: {'peptide': 98}
          Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 94}
    Chain: "D"
      Number of atoms: 871
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 871
          Classifications: {'peptide': 111}
          Link IDs: {'PTRANS': 6, 'TRANS': 104}
    Chain: "E"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "C"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 3.85, per 1000 atoms: 0.69
  Number of scatterers: 5586
  At special positions: 0
  Unit cell: (117.41, 97.4064, 101.755, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      43     16.00
     O    1086      8.00
     N     943      7.00
     C    3514      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=14, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  37 " - pdb=" SG  CYS A 110 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  64 " - pdb=" SG  CYS A 196 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  85 " - pdb=" SG  CYS A 123 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  96 " - pdb=" SG  CYS B 199 " distance=2.25
    Simple disulfide: pdb=" SG  CYS B  50 " - pdb=" SG  CYS B  90 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 131 " - pdb=" SG  CYS B 142 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 170 " - pdb=" SG  CYS B 193 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 300 " - pdb=" SG  CYS B 327 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  28 " - pdb=" SG  CYS C 114 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C  51 " - pdb=" SG  CYS C 101 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  59 " - pdb=" SG  CYS C 105 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D  29 " - pdb=" SG  CYS D  87 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  52 " - pdb=" SG  CYS D  62 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  80 " - pdb=" SG  CYS D  86 " distance=2.05

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG E   1 " - " NAG E   2 "
      " NAG E   2 " - " BMA E   3 "
    NAG-ASN
      " NAG C 401 " - " ASN C  48 "
      " NAG E   1 " - " ASN B 222 "
  Time building additional restraints: 1.44
  Conformation dependent library (CDL) restraints added in 671.6 milliseconds
  

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1332

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 13 sheets defined
      17.4% alpha, 31.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.67
  Creating SS restraints...
    Processing helix  chain 'A' and resid 35 through 59
    Processing helix  chain 'A' and resid 80 through 85
    Processing helix  chain 'A' and resid 117 through 147
      removed outlier: 4.010A  pdb=" N   MET A 147 " --> pdb=" O   ALA A 143 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 156 through 171
    Processing helix  chain 'A' and resid 187 through 218
      removed outlier: 3.937A  pdb=" N   THR A 191 " --> pdb=" O   ASP A 187 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 81 through 85
    Processing helix  chain 'B' and resid 228 through 233
    Processing sheet with id=AA1, first strand: chain 'B' and resid 23 through 27
      removed outlier: 6.270A  pdb=" N   ILE B  23 " --> pdb=" O   GLU B  34 " (cutoff:3.500A)
      removed outlier: 7.373A  pdb=" N   GLU B  34 " --> pdb=" O   ILE B  23 " (cutoff:3.500A)
      removed outlier: 5.408A  pdb=" N   GLU B  25 " --> pdb=" O   VAL B  32 " (cutoff:3.500A)
      removed outlier: 6.258A  pdb=" N   VAL B  32 " --> pdb=" O   GLU B  25 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   LYS B  27 " --> pdb=" O   VAL B  30 " (cutoff:3.500A)
      removed outlier: 6.085A  pdb=" N   TYR B  31 " --> pdb=" O   LEU B 103 " (cutoff:3.500A)
      removed outlier: 7.362A  pdb=" N   HIS B 105 " --> pdb=" O   TYR B  31 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   VAL B  33 " --> pdb=" O   HIS B 105 " (cutoff:3.500A)
      removed outlier: 7.181A  pdb=" N   LYS B 107 " --> pdb=" O   VAL B  33 " (cutoff:3.500A)
      removed outlier: 6.301A  pdb=" N   LEU B  35 " --> pdb=" O   LYS B 107 " (cutoff:3.500A)
      removed outlier: 5.232A  pdb=" N   VAL B  96 " --> pdb=" O   LYS B  92 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   LYS B  92 " --> pdb=" O   VAL B  96 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   HIS B  91 " --> pdb=" O   THR B  59 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   GLY B  70 " --> pdb=" O   TRP B  60 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 23 through 27
      removed outlier: 6.270A  pdb=" N   ILE B  23 " --> pdb=" O   GLU B  34 " (cutoff:3.500A)
      removed outlier: 7.373A  pdb=" N   GLU B  34 " --> pdb=" O   ILE B  23 " (cutoff:3.500A)
      removed outlier: 5.408A  pdb=" N   GLU B  25 " --> pdb=" O   VAL B  32 " (cutoff:3.500A)
      removed outlier: 6.258A  pdb=" N   VAL B  32 " --> pdb=" O   GLU B  25 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   LYS B  27 " --> pdb=" O   VAL B  30 " (cutoff:3.500A)
      removed outlier: 6.085A  pdb=" N   TYR B  31 " --> pdb=" O   LEU B 103 " (cutoff:3.500A)
      removed outlier: 7.362A  pdb=" N   HIS B 105 " --> pdb=" O   TYR B  31 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   VAL B  33 " --> pdb=" O   HIS B 105 " (cutoff:3.500A)
      removed outlier: 7.181A  pdb=" N   LYS B 107 " --> pdb=" O   VAL B  33 " (cutoff:3.500A)
      removed outlier: 6.301A  pdb=" N   LEU B  35 " --> pdb=" O   LYS B 107 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 49
    Processing sheet with id=AA4, first strand: chain 'B' and resid 130 through 133
      removed outlier: 6.526A  pdb=" N   GLU B 188 " --> pdb=" O   SER B 176 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 152 through 153
    Processing sheet with id=AA6, first strand: chain 'B' and resid 156 through 160
    Processing sheet with id=AA7, first strand: chain 'B' and resid 239 through 245
      removed outlier: 5.333A  pdb=" N   ASN B 240 " --> pdb=" O   GLU B 257 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   GLU B 257 " --> pdb=" O   ASN B 240 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 289 through 291
      removed outlier: 4.262A  pdb=" N   ALA B 304 " --> pdb=" O   CYS B 327 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   CYS B 327 " --> pdb=" O   ALA B 304 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   ILE B 306 " --> pdb=" O   VAL B 325 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 31 through 34
    Processing sheet with id=AB1, first strand: chain 'C' and resid 40 through 42
      removed outlier: 5.755A  pdb=" N   ILE C  41 " --> pdb=" O   GLY C 121 " (cutoff:3.500A)
      removed outlier: 5.551A  pdb=" N   GLN C 112 " --> pdb=" O   LEU C 103 " (cutoff:3.500A)
      removed outlier: 6.081A  pdb=" N   LEU C 103 " --> pdb=" O   GLN C 112 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   CYS C 114 " --> pdb=" O   CYS C 101 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   GLY C  95 " --> pdb=" O   VAL C 120 " (cutoff:3.500A)
      removed outlier: 6.125A  pdb=" N   LEU C  68 " --> pdb=" O   PHE C  79 " (cutoff:3.500A)
      removed outlier: 4.766A  pdb=" N   PHE C  79 " --> pdb=" O   LEU C  68 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   LEU C  70 " --> pdb=" O   ILE C  77 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 47 through 56
      removed outlier: 4.035A  pdb=" N   LEU D  50 " --> pdb=" O   SER D  63 " (cutoff:3.500A)
      removed outlier: 6.575A  pdb=" N   SER D  63 " --> pdb=" O   LEU D  50 " (cutoff:3.500A)
      removed outlier: 4.539A  pdb=" N   CYS D  52 " --> pdb=" O   GLU D  61 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   GLU D  61 " --> pdb=" O   CYS D  52 " (cutoff:3.500A)
      removed outlier: 5.197A  pdb=" N   ARG D  54 " --> pdb=" O   ARG D  59 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   ARG D  59 " --> pdb=" O   ARG D  54 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 87 through 88
    Processing sheet with id=AB4, first strand: chain 'D' and resid 87 through 88
      removed outlier: 3.765A  pdb=" N   VAL D 111 " --> pdb=" O   LEU D 131 " (cutoff:3.500A)

    204 hydrogen bonds defined for protein.
    543 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.42

  Time building geometry restraints manager: 1.69 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.20 -     1.32: 1072
        1.32 -     1.45: 1396
        1.45 -     1.57: 3181
        1.57 -     1.69: 0
        1.69 -     1.82: 55
  Bond restraints: 5704
  Sorted by residual:
  bond pdb=" CA  VAL D 107 "
       pdb=" CB  VAL D 107 "
    ideal  model  delta    sigma   weight residual
    1.537  1.479  0.058 1.24e-02 6.50e+03 2.20e+01
  bond pdb=" CA  VAL D 105 "
       pdb=" CB  VAL D 105 "
    ideal  model  delta    sigma   weight residual
    1.541  1.488  0.053 1.30e-02 5.92e+03 1.65e+01
  bond pdb=" CA  PRO B 237 "
       pdb=" C   PRO B 237 "
    ideal  model  delta    sigma   weight residual
    1.514  1.536 -0.022 5.50e-03 3.31e+04 1.60e+01
  bond pdb=" N   VAL B 325 "
       pdb=" CA  VAL B 325 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.035 9.00e-03 1.23e+04 1.54e+01
  bond pdb=" N   THR B  52 "
       pdb=" CA  THR B  52 "
    ideal  model  delta    sigma   weight residual
    1.453  1.489 -0.035 9.20e-03 1.18e+04 1.49e+01
  ... (remaining 5699 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.13: 6213
        2.13 -     4.26: 1422
        4.26 -     6.38: 77
        6.38 -     8.51: 7
        8.51 -    10.64: 2
  Bond angle restraints: 7721
  Sorted by residual:
  angle pdb=" N   ARG C  65 "
        pdb=" CA  ARG C  65 "
        pdb=" C   ARG C  65 "
      ideal   model   delta    sigma   weight residual
     114.62  106.84    7.78 1.14e+00 7.69e-01 4.65e+01
  angle pdb=" C   THR D 123 "
        pdb=" CA  THR D 123 "
        pdb=" CB  THR D 123 "
      ideal   model   delta    sigma   weight residual
     110.78  100.14   10.64 1.60e+00 3.91e-01 4.42e+01
  angle pdb=" CA  GLY B  72 "
        pdb=" C   GLY B  72 "
        pdb=" O   GLY B  72 "
      ideal   model   delta    sigma   weight residual
     122.23  117.93    4.30 6.90e-01 2.10e+00 3.89e+01
  angle pdb=" CA  THR D 112 "
        pdb=" C   THR D 112 "
        pdb=" O   THR D 112 "
      ideal   model   delta    sigma   weight residual
     121.81  115.62    6.19 1.18e+00 7.18e-01 2.75e+01
  angle pdb=" N   SER D 106 "
        pdb=" CA  SER D 106 "
        pdb=" C   SER D 106 "
      ideal   model   delta    sigma   weight residual
     109.59  117.10   -7.51 1.47e+00 4.63e-01 2.61e+01
  ... (remaining 7716 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.20: 3301
       20.20 -    40.40: 196
       40.40 -    60.60: 37
       60.60 -    80.80: 8
       80.80 -   101.00: 6
  Dihedral angle restraints: 3548
    sinusoidal: 1498
      harmonic: 2050
  Sorted by residual:
  dihedral pdb=" CB  CYS C  59 "
           pdb=" SG  CYS C  59 "
           pdb=" SG  CYS C 105 "
           pdb=" CB  CYS C 105 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  166.24  -73.24     1      1.00e+01 1.00e-02 6.83e+01
  dihedral pdb=" CB  CYS B 300 "
           pdb=" SG  CYS B 300 "
           pdb=" SG  CYS B 327 "
           pdb=" CB  CYS B 327 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -147.42   61.42     1      1.00e+01 1.00e-02 5.01e+01
  dihedral pdb=" CB  CYS B  50 "
           pdb=" SG  CYS B  50 "
           pdb=" SG  CYS B  90 "
           pdb=" CB  CYS B  90 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  153.54  -60.54     1      1.00e+01 1.00e-02 4.88e+01
  ... (remaining 3545 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.076: 396
       0.076 -    0.151: 318
       0.151 -    0.227: 119
       0.227 -    0.302: 38
       0.302 -    0.378: 3
  Chirality restraints: 874
  Sorted by residual:
  chirality pdb=" CA  THR D 123 "
            pdb=" N   THR D 123 "
            pdb=" C   THR D 123 "
            pdb=" CB  THR D 123 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.90   -0.38 2.00e-01 2.50e+01 3.57e+00
  chirality pdb=" CA  ASN B 184 "
            pdb=" N   ASN B 184 "
            pdb=" C   ASN B 184 "
            pdb=" CB  ASN B 184 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.32e+00
  chirality pdb=" CB  VAL B 180 "
            pdb=" CA  VAL B 180 "
            pdb=" CG1 VAL B 180 "
            pdb=" CG2 VAL B 180 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.29   -0.34 2.00e-01 2.50e+01 2.96e+00
  ... (remaining 871 not shown)

  Planarity restraints: 979
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER D 100 "   -0.015 2.00e-02 2.50e+03   3.04e-02 9.22e+00
        pdb=" C   SER D 100 "    0.053 2.00e-02 2.50e+03
        pdb=" O   SER D 100 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   ASP D 101 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B 196 "   -0.014 2.00e-02 2.50e+03   2.96e-02 8.76e+00
        pdb=" C   ASP B 196 "    0.051 2.00e-02 2.50e+03
        pdb=" O   ASP B 196 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   SER B 197 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO B 265 "    0.014 2.00e-02 2.50e+03   2.80e-02 7.83e+00
        pdb=" C   PRO B 265 "   -0.048 2.00e-02 2.50e+03
        pdb=" O   PRO B 265 "    0.018 2.00e-02 2.50e+03
        pdb=" N   HIS B 266 "    0.016 2.00e-02 2.50e+03
  ... (remaining 976 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 138
        2.68 -     3.23: 4878
        3.23 -     3.79: 8010
        3.79 -     4.34: 11305
        4.34 -     4.90: 17923
  Nonbonded interactions: 42254
  Sorted by model distance:
  nonbonded pdb=" CD2 LEU B 117 "
            pdb=" CG2 THR B 146 "
     model   vdw
     2.122 3.880
  nonbonded pdb=" CG2 THR B 141 "
            pdb=" OE1 GLU B 192 "
     model   vdw
     2.338 3.460
  nonbonded pdb=" O   ASP A 187 "
            pdb=" OD1 ASP A 187 "
     model   vdw
     2.339 3.040
  nonbonded pdb=" NZ  LYS B 157 "
            pdb=" OD2 ASP B 213 "
     model   vdw
     2.340 3.120
  nonbonded pdb=" O5  NAG C 401 "
            pdb=" O6  NAG C 401 "
     model   vdw
     2.447 2.432
  ... (remaining 42249 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.790
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     16.950
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7351
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.013   0.216   5722  Z= 1.002
  Angle     :  1.644  29.628   7761  Z= 1.216
  Chirality :  0.114   0.378    874
  Planarity :  0.005   0.030    977
  Dihedral  : 13.654 100.996   2174
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 10.81 %
    Favored  : 87.44 %
  Cbeta Deviations :  0.60 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.53 (0.32), residues: 687
  helix:  3.02 (0.48), residues: 119
  sheet:  0.51 (0.35), residues: 230
  loop : -0.76 (0.32), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.003   TRP B  60 
 HIS   0.004   0.001   HIS A  71 
 PHE   0.026   0.002   PHE D  99 
 TYR   0.025   0.002   TYR B 268 
 ARG   0.004   0.001   ARG A 205 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01318 (    2)
  link_NAG-ASN         : angle       5.06095 (    6)
  link_BETA1-4         : bond        0.01249 (    2)
  link_BETA1-4         : angle       2.26960 (    6)
  hydrogen bonds       : bond        0.20263 (  195)
  hydrogen bonds       : angle       8.79343 (  543)
  SS BOND              : bond        0.05808 (   14)
  SS BOND              : angle       5.92036 (   28)
  covalent geometry    : bond        0.01306 ( 5704)
  covalent geometry    : angle       1.60222 ( 7721)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 176
  time to evaluate  : 0.630 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 THR cc_start: 0.8516 (p) cc_final: 0.8123 (p)
REVERT: B  114 THR cc_start: 0.8475 (m) cc_final: 0.8270 (p)
REVERT: B  271 LEU cc_start: 0.8973 (mt) cc_final: 0.8768 (mt)
REVERT: B  275 VAL cc_start: 0.8284 (OUTLIER) cc_final: 0.8017 (m)
REVERT: B  276 GLN cc_start: 0.7301 (tt0) cc_final: 0.7020 (pp30)
REVERT: D   51 ARG cc_start: 0.8152 (ttm170) cc_final: 0.7787 (ptp-110)
REVERT: D   63 SER cc_start: 0.8564 (t) cc_final: 0.8130 (m)
REVERT: D   65 GLN cc_start: 0.7776 (tt0) cc_final: 0.7498 (mt0)
REVERT: D   96 ARG cc_start: 0.7965 (ptp-170) cc_final: 0.7495 (ptp90)
REVERT: D   98 GLN cc_start: 0.8315 (mt0) cc_final: 0.7879 (mt0)
  outliers start: 11
  outliers final: 1
  residues processed: 183
  average time/residue: 0.1967
  time to fit residues: 45.2922
Evaluate side-chains
  113 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 111
  time to evaluate  : 0.625 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain D residue  107 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 57 optimal weight:    0.3980
   chunk 51 optimal weight:    0.8980
   chunk 28 optimal weight:    2.9990
   chunk 17 optimal weight:    0.5980
   chunk 34 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9990
   chunk 53 optimal weight:    0.0470
   chunk 20 optimal weight:    7.9990
   chunk 32 optimal weight:    0.8980
   chunk 39 optimal weight:    0.0670
   chunk 61 optimal weight:    4.9990
   overall best weight:    0.3616

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B  78 GLN
B  87 GLN
B  99 HIS
D 102 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.171401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.141536 restraints weight = 6761.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.140768 restraints weight = 6315.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.141493 restraints weight = 5860.542|
|-----------------------------------------------------------------------------|
r_work (final): 0.3563
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7775
moved from start:          0.2555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   5722  Z= 0.142
  Angle     :  0.617   8.032   7761  Z= 0.328
  Chirality :  0.042   0.157    874
  Planarity :  0.004   0.040    977
  Dihedral  :  7.781  64.229    836
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 16.53 %
    Favored  : 81.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.32), residues: 687
  helix:  3.55 (0.43), residues: 109
  sheet:  0.59 (0.35), residues: 226
  loop : -0.67 (0.31), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP D 118 
 HIS   0.008   0.001   HIS B  91 
 PHE   0.012   0.001   PHE A 118 
 TYR   0.024   0.002   TYR B 314 
 ARG   0.005   0.001   ARG C  75 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00426 (    2)
  link_NAG-ASN         : angle       3.72930 (    6)
  link_BETA1-4         : bond        0.01115 (    2)
  link_BETA1-4         : angle       2.16359 (    6)
  hydrogen bonds       : bond        0.06178 (  195)
  hydrogen bonds       : angle       6.06529 (  543)
  SS BOND              : bond        0.00370 (   14)
  SS BOND              : angle       2.32753 (   28)
  covalent geometry    : bond        0.00299 ( 5704)
  covalent geometry    : angle       0.59011 ( 7721)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 107
  time to evaluate  : 0.609 
Fit side-chains
   revert: symmetry clash
REVERT: A  157 GLN cc_start: 0.6775 (OUTLIER) cc_final: 0.6441 (mp10)
REVERT: B  114 THR cc_start: 0.8430 (m) cc_final: 0.8072 (p)
REVERT: B  271 LEU cc_start: 0.8870 (mt) cc_final: 0.8651 (mt)
REVERT: B  288 ARG cc_start: 0.7347 (ptp-170) cc_final: 0.6691 (mtt180)
REVERT: D   98 GLN cc_start: 0.8429 (mt0) cc_final: 0.8205 (mt0)
REVERT: D  123 THR cc_start: 0.7222 (OUTLIER) cc_final: 0.7020 (m)
  outliers start: 15
  outliers final: 7
  residues processed: 114
  average time/residue: 0.1800
  time to fit residues: 26.6805
Evaluate side-chains
  102 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 93
  time to evaluate  : 0.657 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue  157 GLN
Chi-restraints excluded: chain B residue   87 GLN
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain C residue   33 VAL
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain D residue  123 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 21 optimal weight:    0.0670
   chunk 6 optimal weight:    0.1980
   chunk 10 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9990
   chunk 33 optimal weight:    7.9990
   chunk 12 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   overall best weight:    0.5518

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
C  39 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.166407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.135496 restraints weight = 6908.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.135067 restraints weight = 8094.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.136275 restraints weight = 7817.983|
|-----------------------------------------------------------------------------|
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.3237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   5722  Z= 0.126
  Angle     :  0.548   7.070   7761  Z= 0.291
  Chirality :  0.040   0.185    874
  Planarity :  0.004   0.040    977
  Dihedral  :  5.608  38.449    834
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 18.92 %
    Favored  : 77.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.66 (0.32), residues: 687
  helix:  3.47 (0.44), residues: 112
  sheet:  0.61 (0.34), residues: 226
  loop : -0.70 (0.32), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  60 
 HIS   0.010   0.001   HIS B  91 
 PHE   0.011   0.001   PHE B 140 
 TYR   0.016   0.002   TYR C  71 
 ARG   0.004   0.000   ARG D  48 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00267 (    2)
  link_NAG-ASN         : angle       3.66006 (    6)
  link_BETA1-4         : bond        0.00941 (    2)
  link_BETA1-4         : angle       1.83939 (    6)
  hydrogen bonds       : bond        0.05136 (  195)
  hydrogen bonds       : angle       5.28148 (  543)
  SS BOND              : bond        0.00695 (   14)
  SS BOND              : angle       1.97799 (   28)
  covalent geometry    : bond        0.00288 ( 5704)
  covalent geometry    : angle       0.52418 ( 7721)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 102
  time to evaluate  : 0.702 
Fit side-chains
REVERT: A  157 GLN cc_start: 0.6646 (OUTLIER) cc_final: 0.6365 (mp10)
REVERT: B  114 THR cc_start: 0.8475 (m) cc_final: 0.7977 (p)
REVERT: B  288 ARG cc_start: 0.7466 (ptp-170) cc_final: 0.7092 (mtt180)
REVERT: D  122 GLN cc_start: 0.7673 (mm-40) cc_final: 0.7405 (mp10)
  outliers start: 20
  outliers final: 9
  residues processed: 116
  average time/residue: 0.1728
  time to fit residues: 26.3314
Evaluate side-chains
  107 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 0.637 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 GLN
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain B residue  277 VAL
Chi-restraints excluded: chain C residue   33 VAL
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain D residue   95 THR
Chi-restraints excluded: chain D residue  107 VAL
Chi-restraints excluded: chain D residue  135 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 51 optimal weight:   10.0000
   chunk 21 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   chunk 3 optimal weight:    5.9990
   chunk 15 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9980
   chunk 16 optimal weight:    0.6980
   chunk 44 optimal weight:    7.9990
   chunk 22 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9990
   chunk 17 optimal weight:    0.7980
   overall best weight:    0.8782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  87 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.160118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.125897 restraints weight = 7049.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.127243 restraints weight = 5872.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.128482 restraints weight = 5247.742|
|-----------------------------------------------------------------------------|
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
moved from start:          0.3886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   5722  Z= 0.141
  Angle     :  0.561   8.510   7761  Z= 0.294
  Chirality :  0.040   0.167    874
  Planarity :  0.004   0.039    977
  Dihedral  :  4.396  24.166    834
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 20.19 %
    Favored  : 77.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.60 (0.32), residues: 687
  helix:  3.26 (0.46), residues: 112
  sheet:  0.62 (0.34), residues: 232
  loop : -0.74 (0.33), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 256 
 HIS   0.011   0.002   HIS B  91 
 PHE   0.015   0.001   PHE B 228 
 TYR   0.014   0.002   TYR C  71 
 ARG   0.003   0.001   ARG B 230 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00217 (    2)
  link_NAG-ASN         : angle       3.61872 (    6)
  link_BETA1-4         : bond        0.00783 (    2)
  link_BETA1-4         : angle       1.69866 (    6)
  hydrogen bonds       : bond        0.04675 (  195)
  hydrogen bonds       : angle       4.85820 (  543)
  SS BOND              : bond        0.00470 (   14)
  SS BOND              : angle       1.82787 (   28)
  covalent geometry    : bond        0.00334 ( 5704)
  covalent geometry    : angle       0.54059 ( 7721)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 94
  time to evaluate  : 0.655 
Fit side-chains
   revert: symmetry clash
REVERT: B  114 THR cc_start: 0.8384 (m) cc_final: 0.8024 (p)
REVERT: B  288 ARG cc_start: 0.7596 (ptp-170) cc_final: 0.7264 (mtt180)
  outliers start: 16
  outliers final: 10
  residues processed: 104
  average time/residue: 0.1680
  time to fit residues: 23.0224
Evaluate side-chains
  101 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 91
  time to evaluate  : 0.642 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   87 GLN
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain C residue   33 VAL
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain D residue   95 THR
Chi-restraints excluded: chain D residue  107 VAL
Chi-restraints excluded: chain D residue  135 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 48 optimal weight:    5.9990
   chunk 18 optimal weight:    2.9990
   chunk 41 optimal weight:    4.9990
   chunk 22 optimal weight:    3.9990
   chunk 38 optimal weight:    0.8980
   chunk 49 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 67 optimal weight:    0.0570
   overall best weight:    1.1904

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B  91 HIS
B 166 GLN
** D  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.158681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.127096 restraints weight = 6885.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.126222 restraints weight = 6309.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.126458 restraints weight = 6173.374|
|-----------------------------------------------------------------------------|
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.4189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   5722  Z= 0.162
  Angle     :  0.563   6.653   7761  Z= 0.294
  Chirality :  0.040   0.182    874
  Planarity :  0.004   0.040    977
  Dihedral  :  4.303  18.569    834
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 20.35 %
    Favored  : 76.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.32), residues: 687
  helix:  3.21 (0.46), residues: 112
  sheet:  0.60 (0.34), residues: 230
  loop : -0.78 (0.33), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  60 
 HIS   0.010   0.002   HIS B  91 
 PHE   0.017   0.001   PHE B 228 
 TYR   0.014   0.001   TYR C  71 
 ARG   0.003   0.000   ARG A 205 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00250 (    2)
  link_NAG-ASN         : angle       3.65074 (    6)
  link_BETA1-4         : bond        0.00821 (    2)
  link_BETA1-4         : angle       1.73804 (    6)
  hydrogen bonds       : bond        0.04658 (  195)
  hydrogen bonds       : angle       4.76201 (  543)
  SS BOND              : bond        0.00460 (   14)
  SS BOND              : angle       1.94205 (   28)
  covalent geometry    : bond        0.00396 ( 5704)
  covalent geometry    : angle       0.54057 ( 7721)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 96
  time to evaluate  : 0.610 
Fit side-chains
   revert: symmetry clash
REVERT: A  157 GLN cc_start: 0.6858 (OUTLIER) cc_final: 0.6570 (mp10)
REVERT: A  215 TYR cc_start: 0.8921 (t80) cc_final: 0.8634 (t80)
REVERT: B  114 THR cc_start: 0.8446 (m) cc_final: 0.8072 (p)
REVERT: B  288 ARG cc_start: 0.7741 (ptp-170) cc_final: 0.7451 (mtt180)
  outliers start: 18
  outliers final: 11
  residues processed: 108
  average time/residue: 0.1706
  time to fit residues: 24.1503
Evaluate side-chains
  102 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 90
  time to evaluate  : 0.644 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 GLN
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain B residue  325 VAL
Chi-restraints excluded: chain C residue   33 VAL
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain D residue   95 THR
Chi-restraints excluded: chain D residue  107 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 19 optimal weight:    0.5980
   chunk 10 optimal weight:    0.8980
   chunk 4 optimal weight:    0.0040
   chunk 12 optimal weight:    1.9990
   chunk 64 optimal weight:    0.7980
   chunk 49 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 18 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 59 optimal weight:    5.9990
   chunk 11 optimal weight:    0.1980
   overall best weight:    0.4792

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B  78 GLN
B 166 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.158479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.122211 restraints weight = 6861.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.124028 restraints weight = 5541.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.125478 restraints weight = 4867.886|
|-----------------------------------------------------------------------------|
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.4383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067   5722  Z= 0.112
  Angle     :  0.527   6.209   7761  Z= 0.275
  Chirality :  0.039   0.184    874
  Planarity :  0.004   0.042    977
  Dihedral  :  4.117  17.531    834
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 20.99 %
    Favored  : 76.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.59 (0.32), residues: 687
  helix:  2.93 (0.46), residues: 118
  sheet:  0.78 (0.35), residues: 219
  loop : -0.79 (0.32), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  60 
 HIS   0.013   0.001   HIS B  91 
 PHE   0.015   0.001   PHE A 172 
 TYR   0.012   0.001   TYR C  71 
 ARG   0.003   0.000   ARG A 205 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00218 (    2)
  link_NAG-ASN         : angle       3.25587 (    6)
  link_BETA1-4         : bond        0.00826 (    2)
  link_BETA1-4         : angle       1.62809 (    6)
  hydrogen bonds       : bond        0.04110 (  195)
  hydrogen bonds       : angle       4.47827 (  543)
  SS BOND              : bond        0.00519 (   14)
  SS BOND              : angle       1.77701 (   28)
  covalent geometry    : bond        0.00265 ( 5704)
  covalent geometry    : angle       0.50748 ( 7721)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 89
  time to evaluate  : 0.643 
Fit side-chains
REVERT: A  157 GLN cc_start: 0.6862 (OUTLIER) cc_final: 0.6592 (mp10)
REVERT: B   49 THR cc_start: 0.7829 (m) cc_final: 0.7592 (p)
REVERT: B  114 THR cc_start: 0.8220 (m) cc_final: 0.7819 (p)
REVERT: B  288 ARG cc_start: 0.7689 (ptp-170) cc_final: 0.7444 (mtt180)
  outliers start: 14
  outliers final: 7
  residues processed: 97
  average time/residue: 0.1845
  time to fit residues: 23.1203
Evaluate side-chains
  94 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 86
  time to evaluate  : 0.640 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 GLN
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain B residue  325 VAL
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain D residue   95 THR
Chi-restraints excluded: chain D residue  107 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 1 optimal weight:    3.9990
   chunk 66 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9980
   chunk 21 optimal weight:    9.9990
   chunk 0 optimal weight:    6.9990
   chunk 34 optimal weight:    5.9990
   chunk 24 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 57 optimal weight:    5.9990
   chunk 41 optimal weight:    0.8980
   chunk 37 optimal weight:    0.7980
   overall best weight:    1.3382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B  78 GLN
B  91 HIS
B 276 GLN
C  78 ASN
D  98 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.152299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.116743 restraints weight = 6908.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.117491 restraints weight = 5684.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.118185 restraints weight = 5296.736|
|-----------------------------------------------------------------------------|
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
moved from start:          0.4710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.066   5722  Z= 0.183
  Angle     :  0.593   6.923   7761  Z= 0.309
  Chirality :  0.042   0.231    874
  Planarity :  0.004   0.044    977
  Dihedral  :  4.301  18.791    834
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 21.78 %
    Favored  : 75.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.32), residues: 687
  helix:  2.81 (0.48), residues: 118
  sheet:  0.60 (0.35), residues: 215
  loop : -0.98 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 256 
 HIS   0.012   0.002   HIS B  91 
 PHE   0.022   0.002   PHE B 228 
 TYR   0.013   0.002   TYR C  71 
 ARG   0.004   0.001   ARG B 230 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00207 (    2)
  link_NAG-ASN         : angle       3.48946 (    6)
  link_BETA1-4         : bond        0.00712 (    2)
  link_BETA1-4         : angle       1.76088 (    6)
  hydrogen bonds       : bond        0.04635 (  195)
  hydrogen bonds       : angle       4.56980 (  543)
  SS BOND              : bond        0.00642 (   14)
  SS BOND              : angle       2.03393 (   28)
  covalent geometry    : bond        0.00452 ( 5704)
  covalent geometry    : angle       0.57176 ( 7721)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 0.679 
Fit side-chains
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.8280 (mmt) cc_final: 0.8071 (mmt)
REVERT: B  114 THR cc_start: 0.8393 (m) cc_final: 0.8011 (p)
REVERT: B  258 TYR cc_start: 0.8692 (m-80) cc_final: 0.8392 (m-80)
REVERT: B  288 ARG cc_start: 0.7810 (ptp-170) cc_final: 0.7545 (mtt180)
  outliers start: 14
  outliers final: 10
  residues processed: 100
  average time/residue: 0.1773
  time to fit residues: 23.3685
Evaluate side-chains
  100 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 90
  time to evaluate  : 0.651 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  325 VAL
Chi-restraints excluded: chain C residue   33 VAL
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain D residue   86 CYS
Chi-restraints excluded: chain D residue   95 THR
Chi-restraints excluded: chain D residue  107 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 52 optimal weight:    0.8980
   chunk 66 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   chunk 3 optimal weight:    3.9990
   chunk 58 optimal weight:    0.6980
   chunk 19 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B  78 GLN
B  91 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.154556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.118690 restraints weight = 6912.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.120449 restraints weight = 5670.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.121323 restraints weight = 5054.978|
|-----------------------------------------------------------------------------|
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.4851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068   5722  Z= 0.131
  Angle     :  0.551   8.097   7761  Z= 0.284
  Chirality :  0.039   0.212    874
  Planarity :  0.004   0.046    977
  Dihedral  :  4.137  17.806    834
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 22.58 %
    Favored  : 75.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.36 (0.32), residues: 687
  helix:  2.83 (0.47), residues: 118
  sheet:  0.61 (0.36), residues: 215
  loop : -0.93 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 143 
 HIS   0.011   0.001   HIS B  91 
 PHE   0.011   0.001   PHE B 228 
 TYR   0.012   0.001   TYR C  71 
 ARG   0.003   0.000   ARG D  51 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00209 (    2)
  link_NAG-ASN         : angle       3.20732 (    6)
  link_BETA1-4         : bond        0.00759 (    2)
  link_BETA1-4         : angle       1.63027 (    6)
  hydrogen bonds       : bond        0.04196 (  195)
  hydrogen bonds       : angle       4.39460 (  543)
  SS BOND              : bond        0.00563 (   14)
  SS BOND              : angle       1.93012 (   28)
  covalent geometry    : bond        0.00321 ( 5704)
  covalent geometry    : angle       0.53056 ( 7721)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 0.652 
Fit side-chains
   revert: symmetry clash
REVERT: A  157 GLN cc_start: 0.6889 (OUTLIER) cc_final: 0.6627 (mp10)
REVERT: B  114 THR cc_start: 0.8275 (m) cc_final: 0.7874 (p)
REVERT: B  258 TYR cc_start: 0.8703 (m-80) cc_final: 0.8407 (m-80)
REVERT: B  288 ARG cc_start: 0.7828 (ptp-170) cc_final: 0.7617 (mtt180)
REVERT: D  128 GLU cc_start: 0.7702 (pp20) cc_final: 0.7011 (pp20)
  outliers start: 13
  outliers final: 10
  residues processed: 96
  average time/residue: 0.1829
  time to fit residues: 22.8735
Evaluate side-chains
  98 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 87
  time to evaluate  : 0.674 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 GLN
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain C residue   33 VAL
Chi-restraints excluded: chain C residue   34 THR
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain D residue   86 CYS
Chi-restraints excluded: chain D residue   95 THR
Chi-restraints excluded: chain D residue  101 ASP
Chi-restraints excluded: chain D residue  107 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 37 optimal weight:    0.8980
   chunk 32 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 56 optimal weight:    7.9990
   chunk 64 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9980
   chunk 22 optimal weight:    5.9990
   chunk 14 optimal weight:    2.9990
   chunk 66 optimal weight:    4.9990
   chunk 60 optimal weight:    0.8980
   overall best weight:    1.3582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B  91 HIS
** B  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.152111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.120594 restraints weight = 6967.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.119861 restraints weight = 8878.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.120791 restraints weight = 8466.055|
|-----------------------------------------------------------------------------|
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
moved from start:          0.5063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.067   5722  Z= 0.183
  Angle     :  0.600   7.902   7761  Z= 0.307
  Chirality :  0.041   0.219    874
  Planarity :  0.004   0.049    977
  Dihedral  :  4.275  18.842    834
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 22.89 %
    Favored  : 74.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.18 (0.32), residues: 687
  helix:  2.69 (0.47), residues: 119
  sheet:  0.48 (0.35), residues: 215
  loop : -1.06 (0.31), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 256 
 HIS   0.011   0.002   HIS B  91 
 PHE   0.021   0.002   PHE B 228 
 TYR   0.012   0.001   TYR C  71 
 ARG   0.004   0.001   ARG B 230 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00133 (    2)
  link_NAG-ASN         : angle       3.36793 (    6)
  link_BETA1-4         : bond        0.00682 (    2)
  link_BETA1-4         : angle       1.71289 (    6)
  hydrogen bonds       : bond        0.04572 (  195)
  hydrogen bonds       : angle       4.48664 (  543)
  SS BOND              : bond        0.00601 (   14)
  SS BOND              : angle       1.97723 (   28)
  covalent geometry    : bond        0.00454 ( 5704)
  covalent geometry    : angle       0.57968 ( 7721)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 91
  time to evaluate  : 0.671 
Fit side-chains
   revert: symmetry clash
REVERT: A  141 MET cc_start: 0.7975 (ttm) cc_final: 0.7747 (ttm)
REVERT: A  157 GLN cc_start: 0.6869 (OUTLIER) cc_final: 0.6601 (mp10)
REVERT: B  258 TYR cc_start: 0.8790 (m-80) cc_final: 0.8514 (m-80)
REVERT: B  288 ARG cc_start: 0.7913 (ptp-170) cc_final: 0.7688 (mtt180)
REVERT: D  128 GLU cc_start: 0.7705 (pp20) cc_final: 0.7044 (pp20)
  outliers start: 14
  outliers final: 12
  residues processed: 99
  average time/residue: 0.1970
  time to fit residues: 25.2628
Evaluate side-chains
  104 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 91
  time to evaluate  : 0.652 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 GLN
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain C residue   33 VAL
Chi-restraints excluded: chain C residue   34 THR
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain D residue   86 CYS
Chi-restraints excluded: chain D residue   95 THR
Chi-restraints excluded: chain D residue  101 ASP
Chi-restraints excluded: chain D residue  107 VAL
Chi-restraints excluded: chain D residue  110 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 66 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9990
   chunk 40 optimal weight:    2.9990
   chunk 30 optimal weight:    0.4980
   chunk 8 optimal weight:    5.9990
   chunk 48 optimal weight:    6.9990
   chunk 24 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   chunk 7 optimal weight:    9.9990
   chunk 57 optimal weight:    2.9990
   overall best weight:    0.8586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B  78 GLN
B  91 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.153124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.117033 restraints weight = 6968.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.118370 restraints weight = 5733.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.118370 restraints weight = 5109.626|
|-----------------------------------------------------------------------------|
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8146
moved from start:          0.5149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066   5722  Z= 0.135
  Angle     :  0.566   8.138   7761  Z= 0.290
  Chirality :  0.040   0.210    874
  Planarity :  0.004   0.052    977
  Dihedral  :  4.197  18.020    834
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 22.58 %
    Favored  : 75.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.20 (0.32), residues: 687
  helix:  2.70 (0.47), residues: 119
  sheet:  0.44 (0.35), residues: 215
  loop : -0.99 (0.31), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 143 
 HIS   0.011   0.001   HIS B  91 
 PHE   0.013   0.001   PHE B 228 
 TYR   0.011   0.001   TYR C  71 
 ARG   0.004   0.000   ARG D  51 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00152 (    2)
  link_NAG-ASN         : angle       3.21505 (    6)
  link_BETA1-4         : bond        0.00776 (    2)
  link_BETA1-4         : angle       1.62529 (    6)
  hydrogen bonds       : bond        0.04207 (  195)
  hydrogen bonds       : angle       4.37331 (  543)
  SS BOND              : bond        0.00536 (   14)
  SS BOND              : angle       1.86483 (   28)
  covalent geometry    : bond        0.00334 ( 5704)
  covalent geometry    : angle       0.54677 ( 7721)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1374 Ramachandran restraints generated.
    687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 89
  time to evaluate  : 0.726 
Fit side-chains
   revert: symmetry clash
REVERT: A  141 MET cc_start: 0.7908 (ttm) cc_final: 0.7648 (ttm)
REVERT: A  157 GLN cc_start: 0.6899 (OUTLIER) cc_final: 0.6633 (mp10)
REVERT: B  258 TYR cc_start: 0.8782 (m-80) cc_final: 0.8512 (m-80)
REVERT: B  288 ARG cc_start: 0.7918 (ptp-170) cc_final: 0.7677 (mtt180)
REVERT: D  128 GLU cc_start: 0.7682 (pp20) cc_final: 0.6975 (pp20)
  outliers start: 15
  outliers final: 12
  residues processed: 97
  average time/residue: 0.1881
  time to fit residues: 23.6482
Evaluate side-chains
  100 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 87
  time to evaluate  : 0.697 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 GLN
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  180 VAL
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain C residue   33 VAL
Chi-restraints excluded: chain C residue   34 THR
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain D residue   86 CYS
Chi-restraints excluded: chain D residue   95 THR
Chi-restraints excluded: chain D residue  101 ASP
Chi-restraints excluded: chain D residue  107 VAL
Chi-restraints excluded: chain D residue  110 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 18 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   chunk 63 optimal weight:    0.9990
   chunk 8 optimal weight:    0.7980
   chunk 21 optimal weight:    7.9990
   chunk 43 optimal weight:    0.2980
   chunk 60 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 13 optimal weight:    0.8980
   chunk 58 optimal weight:    0.0050
   chunk 48 optimal weight:    6.9990
   overall best weight:    0.5794

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 217 ASN
B  91 HIS
C  78 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.154093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.117988 restraints weight = 6969.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.119746 restraints weight = 5695.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.120646 restraints weight = 5061.335|
|-----------------------------------------------------------------------------|
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.5238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   5722  Z= 0.115
  Angle     :  0.543   8.182   7761  Z= 0.278
  Chirality :  0.039   0.200    874
  Planarity :  0.004   0.053    977
  Dihedral  :  4.074  17.673    834
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 22.10 %
    Favored  : 75.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.32), residues: 687
  helix:  2.83 (0.47), residues: 119
  sheet:  0.51 (0.36), residues: 217
  loop : -0.92 (0.32), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 256 
 HIS   0.012   0.001   HIS B  91 
 PHE   0.011   0.001   PHE B 140 
 TYR   0.010   0.001   TYR B 314 
 ARG   0.006   0.000   ARG D  48 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00157 (    2)
  link_NAG-ASN         : angle       2.97067 (    6)
  link_BETA1-4         : bond        0.00695 (    2)
  link_BETA1-4         : angle       1.52990 (    6)
  hydrogen bonds       : bond        0.03840 (  195)
  hydrogen bonds       : angle       4.25836 (  543)
  SS BOND              : bond        0.00529 (   14)
  SS BOND              : angle       1.76976 (   28)
  covalent geometry    : bond        0.00279 ( 5704)
  covalent geometry    : angle       0.52539 ( 7721)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2178.16 seconds
wall clock time: 38 minutes 43.03 seconds (2323.03 seconds total)